Is DPP6 p.Leu100= (c.298C>T) pathogenic?

DPP6 p.Leu100= (c.298C>T) is classified Uncertain significance in DPP6 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-22). Absent from gnomAD v4.1; Associated with intellectual disability, autosomal dominant 33.

What condition is associated with DPP6 p.Leu100= (c.298C>T)?

DPP6 p.Leu100= (c.298C>T) is associated with intellectual disability, autosomal dominant 33 (ClinVar).

How common is DPP6 p.Leu100= (c.298C>T) in the general population?

DPP6 p.Leu100= (c.298C>T) is absent from gnomAD v4.1 (gnomAD).

DPP6 p.Leu100=

c.298C>T · VCV4078527

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,132)

Conditions

intellectual disability, autosomal dominant 33

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.17	GERP -1.1, phastCons 0.007
Overall
CADD	3.361	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,612,132). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DPP6
Protein: p.Leu100=
Coding: c.298C>T
MANE Select: NM_130797
Type: single nucleotide variant
Location: chr7:154446268 (GRCh38)
Gene constraint: LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 87.41 · 8 PDB
Residue 100: an α-helix

Full DPP6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, autosomal dominant 33 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DPP6 p.Lys223Arg Uncertain significance ★★ ⚠ same condition
DPP6 p.Pro229Thr Uncertain significance ★★ ⚠ same condition
DPP6 p.Gln271= Benign ★★ same condition
DPP6 p.Lys241= Benign ★★ same condition
DPP6 p.Arg775Ter Likely pathogenic ★ same condition
DPP6 p.Tyr205Ter Likely pathogenic ★ same condition
DPP6 c.2304+2T>C Uncertain significance ★ same condition
DPP6 c.457+3G>A Uncertain significance ★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dpp6-p-leu100 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown